The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community.
academic.oup.com/bioinformati...
In parallel, we’ll continue expanding benchmarks and developing new applications.
Interested in contributing? Reach out! ⬇️
academic.oup.com/bioinformati...
In parallel, we’ll continue expanding benchmarks and developing new applications.
Interested in contributing? Reach out! ⬇️
February 20, 2025 at 4:30 PM
The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community.
academic.oup.com/bioinformati...
In parallel, we’ll continue expanding benchmarks and developing new applications.
Interested in contributing? Reach out! ⬇️
academic.oup.com/bioinformati...
In parallel, we’ll continue expanding benchmarks and developing new applications.
Interested in contributing? Reach out! ⬇️
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
November 26, 2024 at 9:44 AM
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
#Postdoc alert! We are looking for motivated individual with experience in computational systems biology to join our NetworkCommons initiative to benchmark and democratise network contextualisation methods across multiple applications. Deadline Dec 17th link here: tinyurl.com/yrrzxa94
Postdoctoral fellow - Petsalaki Group - NetworkCommons
Your group The Petsalaki, Saez-Rodriguez (EMBL-EBI) and Korcsmáros (Imperial College) groups develop cutting-edge computational and AI approaches to unravel cellular signalling and gene regulation fro...
tinyurl.com
November 26, 2025 at 5:05 PM
#Postdoc alert! We are looking for motivated individual with experience in computational systems biology to join our NetworkCommons initiative to benchmark and democratise network contextualisation methods across multiple applications. Deadline Dec 17th link here: tinyurl.com/yrrzxa94
NetworkCommons is out! It's been a lot of fun to work on this project, please consider contributing to this exciting initiative to democratise network biology 🪐
Thanks a lot to all coauthors especially Denes, @martingarridorc.bsky.social and @juliosaezrod.bsky.social
Thanks a lot to all coauthors especially Denes, @martingarridorc.bsky.social and @juliosaezrod.bsky.social
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
November 26, 2024 at 10:32 AM
NetworkCommons is out! It's been a lot of fun to work on this project, please consider contributing to this exciting initiative to democratise network biology 🪐
Thanks a lot to all coauthors especially Denes, @martingarridorc.bsky.social and @juliosaezrod.bsky.social
Thanks a lot to all coauthors especially Denes, @martingarridorc.bsky.social and @juliosaezrod.bsky.social
NetworkCommons is out! This initiative aims to enhance programmatic interoperability between data, knowledge and methods with the hope of developing more robust benchmarks in the future. Shout out to @vicpaton.bsky.social and Denes for their amazing work here 👇
We present NetworkCommons, a unified platform 🪐 for network biology, providing access to omics data, knowledge, and contextualization methods, all with a consistent API 👇🧵
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
Paper: doi.org/10.1101/2024...
Docs: networkcommons.readthedocs.io
November 26, 2024 at 1:29 PM
NetworkCommons is out! This initiative aims to enhance programmatic interoperability between data, knowledge and methods with the hope of developing more robust benchmarks in the future. Shout out to @vicpaton.bsky.social and Denes for their amazing work here 👇
Hot of the press!! Whether you feel your data can benefit from network biology, you’re a method developer, or you have some strategies to evaluate networks, check this out! NetworkCommons is actively looking for contributions :)
The first version of NetworkCommons is now published in Bioinformatics. Next, we’ll focus on involving more of the network biology community.
academic.oup.com/bioinformati...
In parallel, we’ll continue expanding benchmarks and developing new applications.
Interested in contributing? Reach out! ⬇️
academic.oup.com/bioinformati...
In parallel, we’ll continue expanding benchmarks and developing new applications.
Interested in contributing? Reach out! ⬇️
February 20, 2025 at 5:44 PM
Hot of the press!! Whether you feel your data can benefit from network biology, you’re a method developer, or you have some strategies to evaluate networks, check this out! NetworkCommons is actively looking for contributions :)
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks
doi.org/10.1101/2024...
#omics #data
doi.org/10.1101/2024...
#omics #data
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks
Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrast...
doi.org
November 26, 2024 at 8:13 PM
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks
doi.org/10.1101/2024...
#omics #data
doi.org/10.1101/2024...
#omics #data
Why NetworkCommons? 🤓 Existing tools are often isolated, limiting reproducibility and innovation. NetworkCommons solves this by standardizing access to data, knowledge, and methods, enabling the sharing and reuse of tools, as well as transparent assessment of method performance.
November 26, 2024 at 9:44 AM
Why NetworkCommons? 🤓 Existing tools are often isolated, limiting reproducibility and innovation. NetworkCommons solves this by standardizing access to data, knowledge, and methods, enabling the sharing and reuse of tools, as well as transparent assessment of method performance.
We also aim to establish synergies with other larger community initiatives. For example, we have drafted an initial example of how to connect pertpy @scverse.bsky.social with NetworkCommons networkcommons.readthedocs.io/en/latest/vi...
November 26, 2024 at 9:44 AM
We also aim to establish synergies with other larger community initiatives. For example, we have drafted an initial example of how to connect pertpy @scverse.bsky.social with NetworkCommons networkcommons.readthedocs.io/en/latest/vi...
Currently, NetworkCommons provides access to knowledge from omnipathdb.org, 4 omics datasets, 7 network inference methods, and 4 benchmarking examples. We also encourage users to bring in their own data, methods, or benchmarks 🧩 📘 Source code: ➡️ github.com/saezlab/netw...
Bridging the gap between data, methods and knowledge in the network inference field — NetworkCommons alpha documentation
networkcommons.readthedocs.io
November 26, 2024 at 9:44 AM
Currently, NetworkCommons provides access to knowledge from omnipathdb.org, 4 omics datasets, 7 network inference methods, and 4 benchmarking examples. We also encourage users to bring in their own data, methods, or benchmarks 🧩 📘 Source code: ➡️ github.com/saezlab/netw...
NEW: Postdoc with @epetsalaki.bsky.social @juliosaezrod.bsky.social and Tamas Korcsmáros
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Postdoctoral fellow - Petsalaki Group - NetworkCommons
Your group The Petsalaki, Saez-Rodriguez (EMBL-EBI) and Korcsmáros (Imperial College) groups develop cutting-edge computational and AI approaches to unravel cellular signalling and gene regulation fro...
embl.wd103.myworkdayjobs.com
November 26, 2025 at 11:07 AM
NEW: Postdoc with @epetsalaki.bsky.social @juliosaezrod.bsky.social and Tamas Korcsmáros
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Benchmark and integrate state-of-the-art network contextualisation methods, combining large-scale transcriptomics, proteomics, and single-cell data
Apply by 17 Dec
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1
Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and netw
www.biorxiv.org
November 25, 2024 at 2:47 PM
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1
NetworkCommons aims to become a meeting point for the community, aiding both researchers to get mechanistic models and developers to compare existing methods. 📩 We welcome contributions of datasets, methods, and evaluation strategies to expand the platform’s utility and impact
November 26, 2024 at 9:44 AM
NetworkCommons aims to become a meeting point for the community, aiding both researchers to get mechanistic models and developers to compare existing methods. 📩 We welcome contributions of datasets, methods, and evaluation strategies to expand the platform’s utility and impact
📊 OmniPath was built for #NetworkBiology. Use it for:
• Network analysis directly in Cytoscape (apps.cytoscape.org/apps/omnipath)
• Mechanistic modeling with Corneto (corneto.org) and NetworkCommons
• Network analysis directly in Cytoscape (apps.cytoscape.org/apps/omnipath)
• Mechanistic modeling with Corneto (corneto.org) and NetworkCommons
September 17, 2025 at 1:10 PM
📊 OmniPath was built for #NetworkBiology. Use it for:
• Network analysis directly in Cytoscape (apps.cytoscape.org/apps/omnipath)
• Mechanistic modeling with Corneto (corneto.org) and NetworkCommons
• Network analysis directly in Cytoscape (apps.cytoscape.org/apps/omnipath)
• Mechanistic modeling with Corneto (corneto.org) and NetworkCommons
Related pathway reconstruction frameworks show growing interest in this problem, and we compare our design to others:
- nf-core/diseasemodulediscovery: doi.org/10.1093/bioi...
- NetworkCommons: doi.org/10.1093/bioi...
/4
- nf-core/diseasemodulediscovery: doi.org/10.1093/bioi...
- NetworkCommons: doi.org/10.1093/bioi...
/4
August 11, 2026 at 3:24 PM
Related pathway reconstruction frameworks show growing interest in this problem, and we compare our design to others:
- nf-core/diseasemodulediscovery: doi.org/10.1093/bioi...
- NetworkCommons: doi.org/10.1093/bioi...
/4
- nf-core/diseasemodulediscovery: doi.org/10.1093/bioi...
- NetworkCommons: doi.org/10.1093/bioi...
/4
It highlights how involving non-experts in building networks empowers communities and democratizes technology, shaping it to serve local needs over commercial interests. #NetworkCommons
May 28, 2025 at 2:20 PM
It highlights how involving non-experts in building networks empowers communities and democratizes technology, shaping it to serve local needs over commercial interests. #NetworkCommons
🔗 Ecosystem
CORNETO is powering LIANA+ (liana-py.readthedocs.io), linking cell–cell communication events to intracellular signaling (@scverse.bsky.social). It’s also at the core of NetworkCommons (networkcommons.readthedocs.io), our community-driven platform for network methods.
CORNETO is powering LIANA+ (liana-py.readthedocs.io), linking cell–cell communication events to intracellular signaling (@scverse.bsky.social). It’s also at the core of NetworkCommons (networkcommons.readthedocs.io), our community-driven platform for network methods.
July 22, 2025 at 3:23 PM
🔗 Ecosystem
CORNETO is powering LIANA+ (liana-py.readthedocs.io), linking cell–cell communication events to intracellular signaling (@scverse.bsky.social). It’s also at the core of NetworkCommons (networkcommons.readthedocs.io), our community-driven platform for network methods.
CORNETO is powering LIANA+ (liana-py.readthedocs.io), linking cell–cell communication events to intracellular signaling (@scverse.bsky.social). It’s also at the core of NetworkCommons (networkcommons.readthedocs.io), our community-driven platform for network methods.
This week in #linz join stadtwerkstatt 84x11 fog manifesto.
Our contributions:
core.servus.at/en/content/n...
#arminmedosch
#networkcommons
#fog
#manifesto
#water
#networks
#chatcontrolle
#mediaart
#arselectronica
With @annakraher.bsky.social @sarahghp.bsky.social and many others
Our contributions:
core.servus.at/en/content/n...
#arminmedosch
#networkcommons
#fog
#manifesto
#water
#networks
#chatcontrolle
#mediaart
#arselectronica
With @annakraher.bsky.social @sarahghp.bsky.social and many others
![╚ Further checks with the servus/AMRO community:
::for "Meet the fog"::
https://stwst84x11.stwst.at/en/meet_the_fog
-> Tomorrow, Tue, 2nd Sep, 17:00
> Postcards against Chat Control @freebliss @aderieg @egarri
-> Thu, 4th Sep, 17:00
NØ School / with Dasha Ilina @dasha & @recyclism
::In the Clouded Exhibition::
> Clarification [Black Lotus XIII] by /g/o/d/ \Pamela Neuwirth \Harald Purrer https://stwst84x11.stwst.at/en/clarification_black_lotus_xiii
> Lost in the Sauce (Illusions in the Fog) by @sarahghp https://stwst84x11.stwst.at/en/lost_in_the_sauce_illusions_in_the_fog](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:5zomx2xxsfdtpzhupj7j2ppz/bafkreig6gf5xodbxex7qpqasf2rgcpqimoylcm5fet42qgjqojd45vmx7m)
September 2, 2025 at 12:09 PM
This week in #linz join stadtwerkstatt 84x11 fog manifesto.
Our contributions:
core.servus.at/en/content/n...
#arminmedosch
#networkcommons
#fog
#manifesto
#water
#networks
#chatcontrolle
#mediaart
#arselectronica
With @annakraher.bsky.social @sarahghp.bsky.social and many others
Our contributions:
core.servus.at/en/content/n...
#arminmedosch
#networkcommons
#fog
#manifesto
#water
#networks
#chatcontrolle
#mediaart
#arselectronica
With @annakraher.bsky.social @sarahghp.bsky.social and many others
This infrastructure package could help in the development of #omics based methods for studying biological #networks.
https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1.full
https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1.full
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks | bioRxiv
Summary We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrastructure for the network biology community that supports the development of better methods and benchmarks, by enhancing interoperability and integration.
Availability and Implementation NetworkCommons is implemented in Python and offers programmatic access to multiple omics datasets, network inference methods, and benchmarking setups. It is a free software, available at <https://github.com/saezlab/networkcommons>.
Contact saezlab{at}ebi.ac.uk, martin.garrido{at}embl.de
Supplementary Data Contribution guidelines, additional figures, and descriptions for data, knowledge, methods, evaluation strategies and their implementation are available in the Supplementary Data and in the NetworkCommons documentation at <https://networkcommons.readthedocs.io/>.
### Competing Interest Statement
JSR reports funding from GSK, Pfizer and Sanofi and fees/honoraria from Travere Therapeutics, Stadapharm, Astex, Pfizer, Grunenthal, Moderna and Owkin.
www.biorxiv.org
November 29, 2024 at 8:36 AM
This infrastructure package could help in the development of #omics based methods for studying biological #networks.
https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1.full
https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1.full
Hello guys, I came across networkcommons two months ago. My supervisor in university of Macau introduced it to be for my msc thesis studies. If you don't mind please I'll be asking some questions directly so as to get a clear understanding on how I can use it for my project in integrating multi omi
May 16, 2025 at 8:12 AM
Hello guys, I came across networkcommons two months ago. My supervisor in university of Macau introduced it to be for my msc thesis studies. If you don't mind please I'll be asking some questions directly so as to get a clear understanding on how I can use it for my project in integrating multi omi
#NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological #networks
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks
Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and network inference methods, facilitating their usage and evaluation. NetworkCommons aims to be an infrast...
www.biorxiv.org
November 26, 2024 at 4:32 AM
#NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological #networks
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Hi @drglazcode.bsky.social , do feel free to open issues in the networkcommons github page: github.com/saezlab/netw...
May 22, 2025 at 2:23 PM
Hi @drglazcode.bsky.social , do feel free to open issues in the networkcommons github page: github.com/saezlab/netw...
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1
Summary: We present NetworkCommons, a platform for integrating prior knowledge, omics data, and netw
www.biorxiv.org
November 25, 2024 at 2:47 PM
NetworkCommons: bridging data, knowledge and methods to build and evaluate context-specific biological networks https://www.biorxiv.org/content/10.1101/2024.11.22.624823v1
Don't Miss #NetworkCommons: Medical Care Aha Moments on October 20: http://eepurl.com/bBPUsr
Don't Miss #NetworkCommons: Medical Care Aha Moments on O...
eepurl.com
November 26, 2024 at 7:23 PM
Don't Miss #NetworkCommons: Medical Care Aha Moments on October 20: http://eepurl.com/bBPUsr